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build(all): update htsjdk jar from 2.14.1 to 2.24.1 #310

Closed holmeso closed 2 years ago

holmeso commented 2 years ago

Description

Update the dependency on the htsjdk jar from from version 2.14.1 to 2.24.1. This is the latest released version of htsjdk (March 2021) https://github.com/samtools/htsjdk The previous version (2.14.1) had restricted access to the FastaSequenceIndexEntry class which will be required by the q3tiledaligner project when getting ready for GRCh38.

re #307

Type of change

Please delete options that are not relevant.

How Has This Been Tested?

Unit tests pass. Should the regression tests fail when running against this version of htsjdk, the differences will need to be examined, and potentially the version of htsjdk reverted back to 2.14.1.

Are WDL Updates Required?

no

Checklist:

ChristinaXu2017 commented 2 years ago

we only need update htsjdk on qpicard project but not other tools which implement qpicard on their build file.

holmeso commented 2 years ago

build files that already refer to qpicard in the dependencies now no longer also refer to the picard jar

holmeso commented 2 years ago

Was getting an intermittent exception when running org.qcmg.qsv.softclip.FindSoftClipClustersMTTest.getProperClipSVs Thought it was due to the picard jar upgrade but it turns our that it happends intermittently with picard.jar.2.14.1 as well.

Stack trace for future reference:

htsjdk.samtools.util.RuntimeIOException
    at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:628)
    at htsjdk.samtools.BAMFileWriter.finish(BAMFileWriter.java:155)
    at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:220)
    at org.qcmg.qsv.util.TestUtil.createHiseqBamFile(TestUtil.java:285)
    at org.qcmg.qsv.softclip.FindSoftClipClustersMTTest.getProperClipSVs(FindSoftClipClustersMTTest.java:47)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:48)
    at org.junit.rules.RunRules.evaluate(RunRules.java:20)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.runTestClass(JUnitTestClassExecutor.java:110)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.execute(JUnitTestClassExecutor.java:58)
    at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.execute(JUnitTestClassExecutor.java:38)
    at org.gradle.api.internal.tasks.testing.junit.AbstractJUnitTestClassProcessor.processTestClass(AbstractJUnitTestClassProcessor.java:62)
    at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51)
    at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
    at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
    at com.sun.proxy.$Proxy2.processTestClass(Unknown Source)
    at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:118)
    at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
    at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:182)
    at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:164)
    at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:413)
    at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
    at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.channels.ClosedByInterruptException
    at java.nio.channels.spi.AbstractInterruptibleChannel.end(AbstractInterruptibleChannel.java:202)
    at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:216)
    at java.nio.channels.Channels.writeFullyImpl(Channels.java:78)
    at java.nio.channels.Channels.writeFully(Channels.java:101)
    at java.nio.channels.Channels.access$000(Channels.java:61)
    at java.nio.channels.Channels$1.write(Channels.java:174)
    at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
    at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
    at htsjdk.samtools.util.BlockCompressedOutputStream.flush(BlockCompressedOutputStream.java:323)
    at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:613)
    ... 51 more